Keep in mind that the auto cutter will cause a significant of canvas debris/dust within your printer. Many people who use the auto cutter have issues with tiny white spots in their prints, where ink was sprayed onto dust that fell off. You can certainly try it, just you'll know the source of the issue if this comes up.
The one thing that annoys me about doing it this way, is having to release the canvas and manually remove and refeed it because the machine will not rewind the canvas to the corrcect printing position with the no cutting option enabled.If you don't do this it will waste about 6 to 8" of canvas at the start of the new print.
I manually cut canvas, and routinely print canvas using my 9900 with minimum margin settings without an issue like you describe. I'm able to hold the down arrow to feed the canvas down, manually cut it, then hold the up arrow to bring it back to its starting position. It typically stops backward feeding like it's done, but if I let go of the up arrow and press it again, it continues moving - but of course stopping at the starting position. I think it periodically stops like this to tension up the roll.